The Spotted Softshell Turtle (Pelodiscus variegatus) has been recognised since 2019 from Vietnam and Hainan Island, China, but little information about its population status and distribution range is currently available. The species has been provisionally listed as Critically Endangered by the Turtle and Tortoise Working Group, although the status has not been officially accepted by the IUCN, due to the threats the species is facing, including habitat loss and degradation, overexploitation for food, competition with other non-native softshell turtles and pollution. To identify conservation priority sites for P. variegatus in mainland Indochina, this study combines molecular analyses and species distribution modelling. Our results show that, in Vietnam, Phong Nha-Ke Bang National Park has the largest suitable area and high probability of species occurrence, followed by Vu Quang National Park and Song Thanh and Ke Go Nature Reserves. In addition, the central provinces, from Thanh Hoa to Thua Thien Hue in Vietnam, constitute a key part of the species distribution and should be prioritised for conservation actions. According to the study’s findings, although P. variegatus is possibly found in Laos, the probability decreases sharply at the border between both countries and there is also a gap in the occurrence of wetlands, arguing for strong natural barriers. Unfortunately, to date, only part of the species potential distribution is protected, while no records are known from protected areas, highlighting the need for extended or even new reserves. To recover natural populations of the species and following the IUCN’s One Plan Approach to Conservation, breeding programmes have been established in Vietnam with a potential to expand to other facilities in the country and abroad. Once suitable sites are identified, offspring can be released into the protected areas to improve the current conservation status of this highly-threatened softshell turtle.